Subtyping tree figure

library(phangorn)

## Loading required package: ape

library(dplyr)

## 
## Attaching package: 'dplyr'
## 
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## 
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

source('./staph_metagenome_tools.R')

You can also embed plots, for example:

Load tree

load("~/dm")
NJ <- nj(dm)
plot(NJ, "unrooted", show.tip.label = FALSE)

Find and label CC_30 lables

Run major groups with beta cutoff of .65

decorate_staph_tree("CC_30",NJ,strains)

decorate_staph_tree("CC_5_5",NJ,strains)

decorate_staph_tree("CC_8_",NJ,strains)

for (i in CCs$Reference.CC){
  decorate_staph_tree(i,NJ,strains)
}

Run major groups with beta cutoff of .80

decorate_staph_tree("CC_30",NJ,strains, cutoff = 0.8, deco = "blue")

decorate_staph_tree("CC_5_5",NJ,strains)

decorate_staph_tree("CC_8_",NJ,strains)

for (i in CCs$Reference.CC){
  decorate_staph_tree(i,NJ,strains,cutoff = 0.8, deco = "blue")
}

Tree figure for grant

plot(NJ, "unrooted", show.tip.label = FALSE)
#cc30
tl <- filter(strains,grepl("CC_30",Reference.CC)) %>% filter(Beta > 0.80) %>% select(Sample.Id.of.0.75X)
tps <- which(NJ$tip.label %in% tl$Sample.Id.of.0.75X)
tiplabels(tip = tps, pch= 20, col = "red")
##CC_5_5
tl <- filter(strains,grepl("CC_5_5",Reference.CC)) %>% filter(Beta > 0.80) %>% select(Sample.Id.of.0.75X)
tps <- which(NJ$tip.label %in% tl$Sample.Id.of.0.75X)
tiplabels(tip = tps, pch= 20, col = "green")
#st8
tl <- filter(strains,grepl("CC_8_8_2",Reference.CC)) %>% filter(Beta > 0.80) %>% select(Sample.Id.of.0.75X)
tps <- which(NJ$tip.label %in% tl$Sample.Id.of.0.75X)
tiplabels(tip = tps, pch= 20, col = "blue")
#st75 argentius
tl <- filter(strains,grepl("CC_75",Reference.CC)) %>% filter(Beta > 0.80) %>% select(Sample.Id.of.0.75X)
tps <- which(NJ$tip.label %in% tl$Sample.Id.of.0.75X)
tiplabels(tip = tps, pch= 20, col = "gray")
#cc133
tl <- filter(strains,grepl("CC_133",Reference.CC)) %>% filter(Beta > 0.80) %>% select(Sample.Id.of.0.75X)
tps <- which(NJ$tip.label %in% tl$Sample.Id.of.0.75X)
tiplabels(tip = tps, pch= 20, col = "orange")
add.scale.bar()

Check for senstivity

tl <- filter(strains,Beta > 0.80) %>% select(Sample.Id.of.0.75X)
plot(NJ, "unrooted", show.tip.label = FALSE, main = "Sensitivity: beta > 0.65")
tps <- which(NJ$tip.label %in% tl$Sample.Id.of.0.75X)
tiplabels(tip = tps, pch= 20, col = "red")